Recently, so-called combinatorial methods have gained great interest as a brute force method for finding desirable compounds. These methods involve creating libraries of related compounds, for example, all possible hexapeptides. The interaction of an antigen with the library is then measured. For example, those peptides that strongly bind to the antigen exhibit molecular recognition of the antigen. Thus, combinatorial properties are comparable with the goal of finding a particular molecule with the desired tailored properties.
A variety of combinatorial approaches have been described. Biological methods involve creating a series of bacteriophages, each with a different peptide on its surface (see Scott, J. K., and Smith, G. P., Science, (1990)249, 386 and Devlin, J. J., Panganiban, L. C., and Devlin, P. E., Science, (1990) 249, 404.) Phages binding to the desired antigen are recovered; by sequencing the DNA of these phages the peptide sequences on their surfaces are determined. These peptides are those that can confer molecular recognition of the antigen.
Chemical methods involve the synthesis of different peptides, usually spatially separated on solid supports. One approach is the synthesis of millions of peptides, each on a separate resin bead (see Lam, K. S. et al., Nature (1991) 354, 82.) An alternative to spatially separated libraries is the use of encoded combinatorial libraries, in which each peptide sequence is labeled by an appended genetic tag (see Brenner, S., and Lerner, R. A., Proc. Natl. Acad. Sci. U.S.A., 89, 5381).
Fodor and coworkers recently described a novel method for synthesizing large numbers of peptides bound to a solid support, by combining the techniques of solid phase peptide synthesis, photolabile protection, and photolithography (see Fodor, S. P. A., Science, (1991) 251,767). Their method, called light activated parallel chemical synthesis, makes possible the systematic synthesis and investigation of a large number of different peptides. Its principal advantage is the ease with which any peptide can be decoded. Merely identifying the spatial coordinates of the desired peptide is sufficient to determine its sequence. However, the technique has some serious disadvantages. The method uses amino acids with photolabile protecting groups. Peptide synthesis involves a new set of chemistries; achieving high yields of the desired peptides will require significant effort. More importantly, the use of photolithographic masks combined with solid phase synthesis is inherently labor intensive, and requires specialized skills and equipment. It is generally conceded that the establishment of this method as a routine is simply not possible, since it involves large investments in both equipment and personnel (see Jung, G., and Beck Sickinger, A. G., Angewandte Chemie,(1992) 31,367).
U.S. patent application Ser. No. 08/008,131, filed Jan. 25, 1993 entitled SYNTHESIS OF CHAIN CHEMICAL COMPOUNDS, describes a related technique (to the Fodor technology described above) which eliminates the drawbacks associated with the use of photographic masks by substituting laser scanning for the photolithographic masking step. By this method portions of a photolabile protected amino acid surface are deprotected by a laser printer beam (such as a 5 mW HeCd laser, 3250 .ANG.). Radiation of wavelengths longer than 3200 .ANG. will not damage the most sensitive amino acid, tryptophan. Control of the spatial coordinates which the laser beam deprotects is accomplished by reflecting the laser beam from a spinning mirror, and employing a shutter to block the beam from the surface when desired. The support is moved perpendicular to the scan lines using a precision optical translator. (see also Nishioka, G. M., "Programmable Laser Activated Parallel Synthesis",[1992] NSF Phase I SBIR Final Report under contract ISI-9160637).
The efficacy of the above described laser printer-photolabile protected amino acids has been demonstrated. Also a 1600 site array was synthesized, simply by scanning 40 times in perpendicular directions. Finally, variations of a simple peptide were synthesized in separate scan lines and characterized by antibody adsorption.
The above described system (now call PROLAPS for Programmable Laser Activated Parallel Synthesis) makes possible the automated synthesis of immobilized peptides libraries requiring little specialized skill on the part of the user. However, PROLAPS retains the disadvantage of using amino acids with photolabile protecting groups. It also retains the disadvantage of requiring 20 separate deprotection steps for each position in a peptide that is to be exhaustively varied. For example, the synthesis of all possible hexapeptides requires 20.times.6=120 separate deprotection, wash, and coupling steps. If each cycle requires 1 hour, then 5 days are required to synthesize the array.